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- PDB-2r4v: Structure of human CLIC2, crystal form A -

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Basic information

Entry
Database: PDB / ID: 2r4v
TitleStructure of human CLIC2, crystal form A
ComponentsChloride intracellular channel protein 2
KeywordsTRANSPORT PROTEIN / chloride intracellular channels / CLIC2 / pore-forming protein / ryanodine receptor / Chloride channel / Ion transport / Ionic channel / Transport / Voltage-gated channel
Function / homology
Function and homology information


positive regulation of binding / glutathione peroxidase activity / chloride transport / chloride channel activity / chloride channel complex / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / Stimuli-sensing channels ...positive regulation of binding / glutathione peroxidase activity / chloride transport / chloride channel activity / chloride channel complex / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / Stimuli-sensing channels / signal transduction / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Chloride intracellular channel protein 2 / Intracellular chloride channel / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Chloride intracellular channel protein 2 / Intracellular chloride channel / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Chloride intracellular channel protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHansen, G. / Cromer, B.A. / Gorman, M.A. / Parker, M.W.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of the Janus Protein Human CLIC2
Authors: Cromer, B.A. / Gorman, M.A. / Hansen, G. / Adams, J.J. / Coggan, M. / Littler, D.R. / Brown, L.J. / Mazzanti, M. / Breit, S.N. / Curmi, P.M.G. / Dulhunty, A.F. / Board, P.G. / Parker, M.W.
History
DepositionSep 2, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 21, 2011Group: Non-polymer description
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chloride intracellular channel protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0083
Polymers28,3931
Non-polymers6152
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.015, 74.722, 79.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chloride intracellular channel protein 2 / XAP121


Mass: 28393.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIC2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15247
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 35%-50% PEG 400, 100mM Tris-HCl, pH8.0, 5mM GSH, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.85→54.55 Å / Num. all: 23149 / Num. obs: 23144 / % possible obs: 93.9 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 31.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.8 / % possible all: 62

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K0M

1k0m


Resolution: 1.85→54.55 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.139 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25038 1115 5.1 %RANDOM
Rwork0.21488 ---
obs0.21665 20592 93.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.893 Å2
Baniso -1Baniso -2Baniso -3
1--2.71 Å20 Å20 Å2
2--0.2 Å20 Å2
3---2.51 Å2
Refinement stepCycle: LAST / Resolution: 1.85→54.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 40 125 2000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221901
X-RAY DIFFRACTIONr_bond_other_d0.0040.021677
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9952574
X-RAY DIFFRACTIONr_angle_other_deg1.16233933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64424.83189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02715317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.777158
X-RAY DIFFRACTIONr_chiral_restr0.2180.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022085
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02373
X-RAY DIFFRACTIONr_nbd_refined0.2170.2398
X-RAY DIFFRACTIONr_nbd_other0.1760.21621
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2896
X-RAY DIFFRACTIONr_nbtor_other0.0860.21011
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2111
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0180.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9211.51460
X-RAY DIFFRACTIONr_mcbond_other0.1841.5446
X-RAY DIFFRACTIONr_mcangle_it1.13921840
X-RAY DIFFRACTIONr_scbond_it1.9423896
X-RAY DIFFRACTIONr_scangle_it2.7324.5734
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 47 -
Rwork0.275 939 -
obs--58.76 %
Refinement TLS params.Method: refined / Origin x: 15.2418 Å / Origin y: 11.3556 Å / Origin z: 18.3028 Å
111213212223313233
T-0.1777 Å2-0.0087 Å2-0.0152 Å2--0.154 Å20.0372 Å2---0.1568 Å2
L3.9576 °21.0739 °2-0.4863 °2-2.9654 °2-1.3286 °2--1.6464 °2
S0.0174 Å °-0.4601 Å °-0.3796 Å °0.0462 Å °-0.1946 Å °-0.2613 Å °-0.0444 Å °0.0116 Å °0.1772 Å °

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